9WJW | pdb_00009wjw

Cryo-EM structure of the GarQ-lmYZ complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the extended-spectrum antimicrobial activity of Garvieacin Q.

Duan, J.Li, D.Zhao, Y.Wang, J.

(2026) Appl Environ Microbiol : e0177325-e0177325

  • DOI: https://doi.org/10.1128/aem.01773-25
  • Primary Citation of Related Structures:  
    9WJR, 9WJU, 9WJW

  • PubMed Abstract: 

    Class IIa and IId bacteriocins are antimicrobial peptides with potential for combating antibiotic-resistant pathogens. However, their species-specific activity, dictated by recognition of the mannose phosphotransferase system (Man-PTS) receptor, often restricts their spectrum. Garvieacin Q/Garvicin Q (GarQ), a newly identified class IId bacteriocin, is unusual in that it targets both Lactococcus garvieae and the non-lactococcal pathogen Listeria monocytogenes , yet the structural basis for this cross-species activity has remained unclear. Using cryo-electron microscopy, we determined the structures of GarQ bound to Man-PTS receptors from Lactococcus garvieae and Listeria monocytogenes . In Lactococcus garvieae , the receptor contains a unique Tudor-like γ+ domain that sterically constrains the N terminus of incoming bacteriocins, thereby enforcing specificity for GarQ while excluding others such as lactococcin A (LcnA). In Listeria monocytogenes , GarQ engages the receptor through the same conserved binding mode, effectively bypassing the unusual species barrier. We further demonstrate that the C-terminal length of GarQ is a critical determinant of pore size and target specificity. Together, these findings uncover the structural mechanism underlying GarQ's atypical extended-spectrum activity and provide a framework for engineering bacteriocins with customized spectra to combat specific pathogens.IMPORTANCEThis study establishes a structural basis for how the extended-spectrum bacteriocin Garvieacin Q (GarQ) circumvents the canonical species-specificity of class II bacteriocins by engaging mannose phosphotransferase system receptors from different bacterial genera through both conserved and divergent binding modes. We identify a previously unknown Tudor-like γ+ domain in the Lactococcus garvieae receptor that sterically restricts the access of other bacteriocins, thereby defining bacteriocin specificity. Moreover, we demonstrate that the C-terminal length of GarQ critically determines pore size and bacterial targets, revealing an engineerable principle for designing synthetic bacteriocins with customized spectra against clinically relevant pathogens.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannose/fructose/sorbose family PTS transporter subunit IICA [auth F],
C [auth S],
F [auth Y]
268Listeria monocytogenesMutation(s): 0 
Gene Names: 
UniProt
Find proteins for S5LAD9 (Listeria monocytogenes)
Explore S5LAD9 
Go to UniProtKB:  S5LAD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS5LAD9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PTS mannose family transporter subunit IIDB [auth G],
D [auth T],
G [auth Z]
303Listeria monocytogenesMutation(s): 0 
Gene Names: E5H26_12035FZW98_07125GIH49_05195IP987_000531
UniProt
Find proteins for A0A1E8EBU8 (Listeria monocytogenes)
Explore A0A1E8EBU8 
Go to UniProtKB:  A0A1E8EBU8
Entity Groups  
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UniProt GroupA0A1E8EBU8
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Prepeptide GarQE [auth A]50Lactococcus garvieaeMutation(s): 0 
Gene Names: garQ
UniProt
Find proteins for H6U5Y1 (Lactococcus garvieae)
Explore H6U5Y1 
Go to UniProtKB:  H6U5Y1
Entity Groups  
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UniProt GroupH6U5Y1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-11-12 
  • Deposition Author(s): Wang, J.W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371254
National Natural Science Foundation of China (NSFC)China32171190

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references